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United Continental Holdings was fined $1.1 million by U.S. regulators for stranding passengers inside planes at Chicago’s O’Hare International Airport, the largest penalty since rules took effect in 2010.

Thirteen United planes with 939 passengers on board were delayed on the ground for more than the three-hour limit during thunderstorms that disrupted the second-busiest U.S. airport on July 13, 2012, the Department of Transportation (DOT) said. At least two planes didn’t have working restrooms, according to a consent order issued Friday.

“It is unacceptable for passengers to be stranded in planes on the tarmac for hours on end,” Transportation Secretary Anthony Foxx said in an emailed statement.

A $900,000 fine against AMR’s American Eagle in 2011, also for delays at O’Hare, had been the largest penalty for violating the tarmac rule.

United Continental, while agreeing to pay the fine, had “no viable options to deplane passengers without risking the safety of both the passengers and ground staff,” said Mary Ryan, a spokeswoman.

United didn’t plan adequately for the situation, didn’t use the plan it had, or contact airport officials and other carriers for assistance, the department said. No competitors at O’Hare violated the three-hour rule that day, it said.

Some delays occurred after the airport had resumed operations, the DOT said. One flight by a partner airline flying as United Express was on the tarmac for more than two hours after the airport reopened for the final time.

Under U.S. rules applying to both domestic and foreign carriers, airlines must return to a gate to give passengers a chance to get off planes that have been stranded on a tarmac longer than three hours.

“We are committed to complying with the tarmac-delay regulations and we continue to improve our procedures while maintaining the safety of our customers and co-workers,” Ryan said.

Thunderstorms with lightning hit O’Hare on July 13, 2012, shutting portions of the airport grounds four separate times from 12:50 p.m. until 6:02 p.m., according to the DOT’s investigation.

With the tarmac closed, United couldn’t get planes in and out of its gates. O’Hare’s policy is to close the areas between the gates and the taxiways whenever lightning strikes within 5 miles of the airport.

As planes continued to land on the runways, few were departing and aircraft stacked up on the ground.

“By that time, the number of arrivals exceeding departures had created untenable gridlock,” the DOT said in the order.

Of the $1.1 million, United must pay the government $475,000. The airline was credited with $185,000 in compensation it made to passengers on the flights. The DOT is allowing the carrier to spend $440,000 of the penalty to purchase a system to track planes on the ground at O’Hare, according to the consent order.

United, with $37.7 billion in revenue for the year ending Sept. 30, won’t see a significant impact from the fine, said George Hamlin, who runs Hamlin Transportation Consulting.

“It’s not pocket change,” Hamlin said. “On the other hand, look at United’s gross revenue. They didn’t stand on their head and turn blue.”

United said that 1,156 of its flights that day at O’Hare were in compliance with U.S. rules, or almost 99 percent of its operations. Since the incident, the airline has added employees at O’Hare and bought new stairs for use in getting passengers off a plane.